RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.YnRvt4/RM_23436.ThuSep121104242024
Search Engine = rmblast 2.13.0+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1726164263
Database = /dev/shm/rModeler.YnRvt4/GCA_900090035.2_PocGH01   - Sequences = 653
  - Bases = 33479509
  - N50 = 1299758
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2749403-2945718 |                                                   [ 2 ]
  2553089-2749403 |                                                   [  ]
  2356775-2553089 |                                                   [  ]
  2160461-2356775 |                                                   [  ]
  1964147-2160461 |                                                   [ 1 ]
  1767833-1964147 |                                                   [ 2 ]
  1571519-1767833 |                                                   [  ]
  1375204-1571518 |                                                   [ 2 ]
  1178890-1375204 |                                                   [ 1 ]
  982576-1178890  |                                                   [ 1 ]
  786262-982576   |                                                   [ 2 ]
  589948-786262   |                                                   [ 3 ]
  393634-589948   |                                                   [  ]
  197320-393634   |                                                   [  ]
  1006-197320     |************************************************** [ 639 ]

Storage Throughput = excellent ( 1219.77 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33479462 bp ( 33388610 non ambiguous )
   - Num Contigs Represented = 653
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:13:31 (hh:mm:ss) Elapsed Time
Round Time: 02:04:33 (hh:mm:ss) Elapsed Time : 96 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1141 repeats masked totaling 1002116 bp(s).
   - TE Masking time 00:01:53 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10049213 bp
       Num Contigs Represented = 223
       Non ambiguous bp:
             Initial: 10021721 bp
             After Masking: 8807984 bp
             Masked: 12.11 % 
 -- Input Database Coverage: 10049213 bp out of 33479509 bp ( 30.02 % )
Sampling Time: 00:02:58 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 73920
Comparison Time: 00:56:37 (hh:mm:ss) Elapsed Time, 14018 HSPs Collected
Number of families returned by RECON: 1186
Round Time: 01:00:28 (hh:mm:ss) Elapsed Time : 7 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4099 repeats masked totaling 2605398 bp(s).
   - TE Masking time 00:03:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 23430169 bp
       Num Contigs Represented = 483
       Non ambiguous bp:
             Initial: 23366809 bp
             After Masking: 20272514 bp
             Masked: 13.24 % 
 -- Input Database Coverage: 33479382 bp out of 33479509 bp ( 100.00 % )
Sampling Time: 00:05:27 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 415416
Comparison Time: 03:05:54 (hh:mm:ss) Elapsed Time, 14968 HSPs Collected
Number of families returned by RECON: 2806
Round Time: 03:13:34 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 114 families found


Classification Time: 00:12:38 (hh:mm:ss) Elapsed Time


Program Time: 06:31:13 (hh:mm:ss) Elapsed Time